[1]:
import os,sys
%matplotlib inline
import matplotlib.pylab as plt
import anndata
import numpy as np
import pandas as pd
plt.rcParams['figure.dpi'] = 100
plt.rcParams['savefig.dpi']=300
plt.rcParams['font.family']='sans serif'
plt.rcParams['font.sans-serif']='Arial'
plt.rcParams['pdf.fonttype']=42
sys.path.append(os.path.expanduser("~/Projects/Github/adataviz/"))
import adataviz as av
print(av.__version__)
0.1
Plot embedding (umap or tsne)ΒΆ
[2]:
adata_path="/home/x-wding2/Projects/BICAN/adata/HMBA_v2/HMBA.Group.downsample_1500.h5ad"
# # adata_path="/home/x-wding2/Projects/BICAN/adata/HMBA_v2/Human_HMBA_basalganglia_AIT_pre-print.h5ad"
palette_path="/home/x-wding2/Projects/BICAN/adata/HMBA_v2/HMBA_color_palette.xlsx"
[3]:
av.pl.interactive_embedding(adata=adata_path,obs=None,variable='Subclass',gene=None,
coord="umap",vmin='p1',vmax='p99',cmap='jet',
width=800,height=600,palette_path=palette_path)
[4]:
av.pl.interactive_embedding(adata_path,obs=None,variable='Group',gene="DRD2",
coord="umap",vmin='p1',vmax='p99',cmap='jet',
width=800,height=700,palette_path=palette_path,size=6)
'prior_mean' not found in obs